We often see that a manufacturer's high-end (D)SLR models offer a "100% viewfinder," which shows the entire exposed frame, and allows precise composition with regard to objects near the edge of the frame.

Lower-end models may instead have a 96% viewfinder, so the exposed frame extends slightly beyond what you see in the viewfinder.

4 Answers
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The main reason is that a 100% viewfinder requires extremely careful adjustment to assure that the framing in the viewfinder exactly matches what will show up on the sensor. In most cases (I'm pretty sure all cases, really) this means they have a little adjustable frame just below the pentaprism that gets adjusted by hand to match up precisely with what the sensor sees. That kind of finicky hand work costs serious money.

The other part is that a 100% viewfinder requires that you build most of the components in the viewfinder optical path a little larger to allow the larger stream of light through. With a 96% (for example) viewfinder, you can make the view-screen, pentaprism, etc., all just a tad smaller saving a bit on materials and such. This undoubtedly makes the biggest difference to the pentaprism, since increasing the area of the viewscreen requires increasing the volume of the prism.

In theory, it's not really related to a pentamirror versus pentaprism -- if you wanted to badly enough, you could (theoretically) build a pentamirror camera with a 100% viewfinder -- but it would be a little like a Tata Nano with a diamond-crusted shift knob.

Exactly. The precision for a 100% is extremely tight and it takes much more effort to make something more precise than it does to make it slightly bigger. The only ones to offer a lower-cost 100% coverage is Pentax because the CCD-Shift system the use for stabilization is used to place the sensor exactly aligned with the viewfinder not vice-versa. In other words they measure what the viewfinder sees and move the sensor there. So it does not require extremely precise measurements at construction time.
– ItaiMay 10 '11 at 2:12

While less influent in digital photography where images can be cropped to a 10x10px section or left with all the detail that was recorded by the camera, photos taken on 135 film ended up being slightly cropped when projected (due to the physical structure of mounts) or printed (since optical printing after all involves a projection stage in the enlarger).

Since negative film is practically unviewable as-is (and slide film is still not in a sane size for direct appreciation of the image) this might have played a role in the segregation of professional cameras due to having an 1:1 as opposed to slightly more conservative framing system…

The main reason many cameras do not have 100% viewfinders is the same reason that they don't all have full frame sensors, huge buffers, and GPS embedded. The same reason that all lenses are not perfect glass, IS, and f/1.0 : cost.

It's all a trade-off. Every camera can have 100% viewfinder, but it might have to give up a feature, or increase the price. This is why the Canon 1D/1Ds, and nikon D3x/s are so expensive: they have no or few compromises.

Edit for coneslayer comments above...I think it reads easier here:

I will amend this response to add that part of the manufactures decision is not only cost but perceived cost and value. Manufacturers of all goods seek to differentiate their offerings and camera vendors do so by offering different features and benefits. We know that nearly all Canon cameras now have the same basic chips inside, but some cameras claim to have more buffer size, etc. It is also just as likely that some simply have different software loads on the same chip, thus reducing parts costs while offering different features via software. Viewfinder view could be one of these differentiators as well, and at least with Nikon and Canon, we see 100% viewfinders on their top end cameras ($5000+), but often not on beginner models. This suggests that its either a differentiator or a cost factor.

Another possible reason is the following: if a manufacturer promises a 100% viewfinder, this suggests a level of precision that is not in a 96% viewfinder. 100% is just that: it must match the exact view that is seen by the sensor. If the prism or mirror or anything in the view path is slightly out of alignment, the photographer may assume something is in the shot that actually isn't. Imagine your surprise if your shot is different and does not include the subject as you saw in the viewfinder. On the other hand, if its a 96% viewfinder, your view will be smaller than the sensor view, and the final shot will include portions of the subject NOT in the viewfinder, giving you ample margin to adjust your image in post as you see fit. With 100%, there is no margin.

I have to assume that the precision to deliver 100% vs 96% is significantly higher here, and more importantly, much higher cost. Alignment issues on an automated line could mean costly scrapping of expensive parts, and hand assembly I would imagine is too costly for volumes needed for Canon xxxxD/xxxD models.

I suppose a vendor could also provide 110%, and draw a box on the viewfinder around the assumed sensor view...but I don't think I have seen this since old rangefinders.

From what others have said (very interesting answers and comments!), we could infer coverage percentage is really related to cost, while viewfinder size is mainly related to other factors, i.e.

people who buy low-end SLRs are most likely to
expect a smaller and
lighter camera; a bigger viewfinder
needs a bigger, heavier body like
those needed for professional gear, that starts to take money.
But the cost of making just some parts (of the
viewfinder) millimeters bigger is not
likely to be relevant.

market segmentation strategies, as
cmason pointed out. Coneslayer said
cmason's point was weak in that he
"compared it to features that really
do have a substantial cost of
implementation". IMHO it's quite
clear that manufacturers
differentiate their products with
both actually expensive features and
things that wouldn't cost them a
penny, e.g. some features in
firmware: in a low-end SLR you can,
say, assign three functions to a
button, in a camera which has double
the price those functions are maybe
ten or nearly any function available in the
menu.

A bigger viewfinder is really useful, but 100% coverage compared to 96% or the like is just one more selling point to please professionals and amateurs who, for different reason and with different expectations, still both of them expecting high standards in every part of their gear, spend thousands $/€ on a top level camera body.

Well, this is not a real answer, just wanted to let out some thoughts I came up with reading other entries, and to respond to some of what others said. Nevertheless I think my post tackles the "why?" part of the question, so it's not entirely off topic.